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Wing disc atlasapi script #595

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Skxsmy
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@Skxsmy Skxsmy commented Jun 25, 2025 •
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Before submitting a pull request (PR), please read the contributing guide.

Please fill out as much of this template as you can, but if you have any problems or questions, just leave a comment and we will help out :)

Description

What is this PR

  • Bug fix
  • Addition of a new feature
  • Other

Why is this PR needed?
Add a new script for packaging wing disc atlas
What does this PR do?
Packaging the newly made wing disc atlas

How has this PR been tested?

locally

Is this a breaking change?

no

Does this PR require an update to the documentation?

no

Checklist:

  • The code has been tested locally
  • Tests have been added to cover all new functionality (unit & integration)
  • The documentation has been updated to reflect any changes
  • The code has been formatted with pre-commit

Skxsmy and others added 14 commits June 20, 2025 13:41
@Skxsmy
Add blank script file for drosophila wing disc atlas script
df424aa
@Skxsmy
First version of wingdisc atlasapi script.
15b7a8b
@Skxsmy
A small functionality added to annotation_utils.py
fe1de66
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
bb9d188 
for more information, see https://pre-commit.ci
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
763a960 
for more information, see https://pre-commit.ci
@Skxsmy
change from imsave to imwrite, updated version requirement for tifffi…
930f7fa 
…le (>=2018.11.6)
@Skxsmy
Merge branch 'wing_disc_script' into annotation_utils
ea7b314
@Skxsmy
Merge branch 'tifffile_version_fix' into wing_disc_script
64f52c9
@Skxsmy
Merge branch 'brainglobe:main' into wing_disc_script
239d6c3
@Skxsmy
Merge remote-tracking branch 'origin/wing_disc_script' into wing_disc…
3d626d3 
…_script
@Skxsmy
DOI value from None to 'unpublished'
980ea7d
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
c614744 
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@Skxsmy
Merge branch 'brainglobe:main' into wing_disc_script
6c4afdb
@Skxsmy
Revert "Merge branch 'wing_disc_script' into annotation_utils"
366f79e 
This reverts commit ea7b314, reversing
changes made to bb9d188.

revert merging of annotation_util branch into this branc

revert merging of annotation_util branch into this branch
@alessandrofelder alessandrofelder self-requested a review July 9, 2025 09:52
@alessandrofelder alessandrofelder marked this pull request as ready for review July 9, 2025 09:52
alessandrofelder
alessandrofelder reviewed Jul 9, 2025
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Once we decide what to name the atlas, the script should be renamed accordingly, but otherwise looks great - thanks @Skxsmy

Mostly updating of the docstrings is needed.

Could you share the wingdisc_annotations.txt file with me, please, so I can run it locally too and check that it works on a different machine too?

brainglobe_atlasapi/atlas_generation/atlas_scripts/L3I_wingdisc.py
Comment on lines +14 to +22
# Copy-paste this script into a new file and fill in the functions to package
# your own atlas.

### Metadata ###

# The minor version of the atlas in the brainglobe_atlasapi, this is internal,
# if this is the first time this atlas has been added the value should be 0
# (minor version is the first number after the decimal point, ie the minor
# version of 1.2 is 2)
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Suggested change
# Copy-paste this script into a new file and fill in the functions to package
# your own atlas.
### Metadata ###
# The minor version of the atlas in the brainglobe_atlasapi, this is internal,
# if this is the first time this atlas has been added the value should be 0
# (minor version is the first number after the decimal point, ie the minor
# version of 1.2 is 2)

And either remove or correct any comments that are not accurate (copy-pasted from the template script).

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wingdisc_annotation.txt

brainglobe_atlasapi/atlas_generation/atlas_scripts/L3I_wingdisc.py

# The orientation of the **original** atlas data, in BrainGlobe convention:
# https://brainglobe.info/documentation/setting-up/image-definition.html#orientation
ORIENTATION = "asr"
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We need to think about orientation! Is this correct?

"asr" stand for Anterior-Superior-Right, and specifies the location of pixel 0,0,0 of the template image. We have a left wing, I think? Where is pixel 0,0,0 in the image, with respect to the body of the drosophila larva?

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Following our internal discussions, I think our best approximation of the orientation is "ras" here. Assumptions around this

  • the line from the centre of the pouch to the centre of the notum points towards anterior
  • the tip of this left wing points slightly medially, ie to its right.
  • the wingdisc plane is approximately flat and parallel to the "back" of the larva
  • the peripodium is dorsal to the rest of the wingdisc

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Documenting our internal discussions that we have settled on drosophila_wingdisc_instar3 for the atlas name, so this script should be named drosophila_wingdisc_instar3.py.

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@Skxsmy @alessandrofelder